In basic terms, when we talk of biological filtration we are actually talking about a 'portion' of the Nitrogen Cycle.

 I.e.

Organic matter (fish waste/Uneaten food/Decaying organisms) ==> ammonia ==> nitrite ==> nitrate ==> nitrogen gas

However, the nitrogen cycle is quite complex, and it would not be easy to show all the combinations of paths and intermediate steps in the cycle. A more comprehensive, but still simple view of the nitrogen cycle is shown in (figure 1:)

(Fig 1)

To understand what is going on during this cycle we need to understand that nitrogen exists all the way through this cycle in many forms, Occasionally as food, and also as a waste product. Algae and plants as autotroph's, can utilise inorganic nitrogenous compounds as a food source (i.e. Nitrite and Nitrate), Whereas Animals are Heterotroph's, I.e. they utilise Organic nitrogen compounds such as algae and particulate waste....Bacteria on the other hand can utilise both organic, and inorganic Nitrogen compounds.

As aquarists, we add organic matter as food for the animals in our care. Organic matter, is matter that is formed by living organisms, contains carbon and may be animal, algal or plant in origin. The animals digest this food and utilise the proteins, fats and  carbohydrates that make up this organic matter. The proteins are broken down into amino acids which can be used to form new proteins or metabolised. The by products of the metabolism of amino acids are carbon dioxide, water and Ammonia/Ammonium (and a few other compounds). Most marine animals excrete ammonia directly into the water. Not all of the ingested organic matter is utilised by the animals and it is excreted as faeces. While most of this food we add is eaten by the animals, either the ones we target feed, or other animals in the aquarium, some food is left uneaten. This food will then be broken down by bacterial action. Another addition to this is the death of any organism be it animal Algal, or bacterial. In this instance the remaining matter may be utilised by scavengers and enter back into the cycle at the 'assimilation' stage or may be broken down again by bacterial action.

When we talk about a 'biological filter', we are actually talking about a living breathing collection of bacteria that are encouraged to work to our benefit in an effort to break down and convert various organic toxins that build up in our water as a by product of the food we introduce and the digestion/metabolic processes of the organisms we keep, and also to assist in the breakdown of accumulating matter both organic and inorganic that is in constant ebb and flow on all the surfaces within our aquarium and the water column itself. All higher organisms present in our aquarium 'i.e. those above algae' actively consume solid matter to some degree or other as food, and digest it to assimilate various compounds for the purpose of tissue growth and to help maintain metabolic processes. What is not needed, or has been converted is excreted as waste, which by and large consists of non digestible matter, various chemicals, dies, and various toxic (in higher concentrations) substances  such as Phosphate (PO4) which restricts the formation of calcareous skeletons in corals etc, and Ammonia/Ammonium (NH3/NH4) which is lethal to nearly all higher organisms. Some of these substances can only be removed using dedicated removal methods whereas others may be broken down or Assimilated/fixed by other methods (i.e. Algae, that take in Nitrate and Phosphate for food).

In relation to the biological breakdown of one of these substances i.e. Ammonia. we can call upon the help of one of mother natures greatest inventions, 'Bacteria'. The bacteria we use to break down this Toxin fall into two main groups called 'Nitrifying' and 'De'-Nitrifying bacteria. or aerobic (oxygen requiring) and anaerobic (Oxygen hating). The first group of aerobic bacteria, are called Nitrosomonas, which actively take Ammonia out of our water and oxidise it / feed on it. The by product of this process is  Nitrite or (N02) Still very harmful to all but the hardiest of creatures but far better than Ammonia. This is then broken down / oxidised by further aerobic bacteria called Nitrobacter to the relatively harmless NO3 or 'Nitrate'. Under suitable conditions, things go a stage further whereby under  levels of severely depleted O2 A further group of bacteria namely De-nitrifying bacteria of the genus  Pseudomonas, Bacillus and Alcaligines, then utilise this nitrate in the same fashion as before which gives of harmless Nitrogen gas or N2 as an end product.

Although it might seem odd that we have to concern ourselves with stocking our aquarium with bacteria rather than fish. In real terms we don't really have a choice in the matter. These bacteria inhabit literally every type of environment on our planet. One way or another, they will eventually find their way in to our aquariums as long as there is a suitable substrate for them to attach themselves to i.e. the side walls/ rocks, and sand. And there is a suitable food source i.e. decomposing matter or fish waste comprising 'among other things' of Ammonia.

When we look closely at aerobic bacteria 'another words they need oxygen'. The relationship between oxygen levels and bacterial levels/activity is very close. I.e.. high O2 levels equate to a high aerobic bacterial activity / colonisation and an effective biological filter hence the need for good circulation and surface agitation with our aquarium. and low levels of dissolved O2 cause a drop in aerobic bacterial activity/ colonisation. To a certain degree, temperature levels are also crucial to this relationship as well, which is due to the fact that extremely high temperatures levels cause a lowering of the waters ability to hold high levels of dissolved O2, whilst extremely low temperatures constitute to a lowering of bacterial activity due to the reduction in the biological/chemical processes within the bacteria themselves, 'just like you and I get lethargic if we are cold '. Items such as skimmers also play a role in how effective your biological filtration works due the skimmers ability to increase the level of dissolved O2 in the water and decrease the amount of CO2 present (as well as directly removing proteins prior to the decomposition process). Fundamentally, most successful systems utilise very strong circulation, a good substrate in the way of a sand layer and Live rock, and very effective skimming to give the best possible environment for bacterial colonisation, and the speedy breakdown of harmful Ammonia to Nitrite, then to Nitrate.

If we look at 'De-nitrification' or the breakdown of Nitrate into free Nitrogen gas, we are looking at a complete opposite in environmental requirements, i.e. these bacteria will only flourish in conditions where O2 levels are severely depleted. We will usually only find these areas in situations such as, the inner recesses of Live Rock, the lower layers of fine sand beds (i.e. below 1-2" deep), inside dedicated nitrate filters or in areas of slack flow across the live rock boundary layer.. In these cases, these bacteria break down Nitrate and nitrite to utilise the Oxygen molecule present in each case. The final by-products of this process are nitrogen N2, and Nitrous oxide N2O. One of the hazards, is that in certain circumstances such as the process being halted mid way, Nitrate may be converted back through the stages to Ammonia. Although this is rare, it can happen in the case of badly adjusted nitrate filters or a disturbed sand layer in the case of DSB’s, hence we should never dig around in a deep sand bed.

 Inevitably achieving both these conditions in a closed environment is the overall challenge, but it can be done if thought out properly.

 There are numerous other aspects to the biological filtration principles and chemical processes going on, however they generally go hand in hand with the situations as stated above so no further action is required over and above these requirements to achieve effective biological filtration. It simply rests on the keeper to decide which methods they wish to employ to get the results as mentioned above.

Biological Filtration and Methodology

To achieve the results as shown above, (i.e. effective breakdown of NH3 - NO2 -NO3 -N2) We can utilise various methods, each with its own benefits or drawbacks. Some methods successfully complete the entire process, whilst others are designed to be very efficient in one specific area. These are as follows.

1 Under gravel filters. or UGF's.

In this case we are forcing water through a layer of fairly coarse coral gravel that sits over a filter plate grid, with the main aim of breaking down waste quickly and efficiently to the NO3 stage. Little to no further breakdown is encountered due to the inherently high O2 levels present with the fast flowing water passing through the gravel layer. Frequent Hoovering and turning of this layer is also required to keep flow at a maximum. In certain respects the UGF also acts as a mechanical filter, trapping waste until it can be removed on a weekly or even daily basis. In this respect the UGF commonly falls short in its ability to offer 'total' biological filtration due to the ever increasing NO3 levels, which require the intervention of the keeper via water changes to dilute the NO3 present, or the utilisation of supplemental Nitrate filters or Macro algae such as Caulerpa to assimilate the rising NO3.

2 Trickle filters.

The trickle filter is an advancement on the UGF principle whereby the media (be it crushed coral gravel/shell or bio media such as bio balls etc) is brought out of the main water column and is held in a tower above the sump where tank water is sprayed or trickled over the media. This has the advantage of massively increasing the air/water interface, and maximising the level of O2 available to the bacteria present.  Much as before, this method will only work up to the NO3 stage  due to the high O2 levels with little to no de-nitrification taking place. But it is supremely efficient at Ammonia and Nitrite breakdown which is why shops use it for dealing with sudden changes in stocking densities as new stock comes in.. IMO this is where the trickle filter stumbles quite often though when used in conjunction with a reef set-up unless specifically designed to utilise it. The mere fact that NO3 production is so efficient, means that if the biomedia is trapping a large degree of waste prior to it being skimmed out, then the system can get a 'bottleneck', whereby NO3 production exceeds the ability of any De-nitrifying bacteria present. Then, NO3 levels can quickly climb to undesirable levels unless other supplementary de-nitrification is offered, or copious water changes are undertaken as preventative maintenance effectively, the system becomes 'imbalanced' in relation to its ability to carry out nitrification and de-nitrification. Systems utilising trickle filters have to be monitored closely in relation to feeding, They can very quickly build up high levels of NO3 in cases where there is overfeeding going on, or a creature dies off unnoticed. In this case, I would always recommend backing up the trickle filter with a subsidiary section utilising a large amount of algae such as Caulerpa, or sea grass, to keep Nitrate levels in check.

3.Deep sand beds and Plenums.

Although covered in detail in the H&T sections. DSB's and plenums offer one of the few methods that successfully complete the 'entire' breakdown process right through to the final nitrogen gas stage. Plus the methods involved in his process means that all breakdown is of an even, or more balanced nature. In my opinion, a combination of DSB/Plenum, and additional use of Macro algae such as Caulerpa, is probably the most effective way 'at present' of ridding a system of excess nutrients to the point that it is quite possible 'if not common' to achieve such low levels that water quality can get very very close to NSW standards.

4. Fluidised bed filters.

In this instance we have again taken the media out of the main aquarium and placed it in a tube with a circulation pump attached. The media in this case is usually very fine sand. The circulation pump pushes tank water up through the media from the bottom which causes the media to 'fluidise' or bubble. The net effect of this action is two fold....Firstly, to increase the supply of O2 to the bacteria present as the sand moves around constantly surrounded by a fresh stream of water. And secondly, the scouring action of the grains as they rub together cleans the old dead bacteria off, to make way for new bacterial growth. Fluidised filters are very efficient at converting ammonia through to Nitrate. Unfortunately, just like trickle filters they lack the ability to go further and the net result is an accumulation of Nitrate which must be removed or kept in check via water changes. Again, I would always recommend backing up the Fluidised filter with a subsidiary section utilising a large amount of algae such as Caulerpa, or sea grass, to keep Nitrate levels in check.

5. Canister filters. Utilising Bio Media.

In this case we have taken our gravel or other suitable media out of the main aquarium again and placed it inside a canister that has a pump attached. Water is then fed through this media where the colonised bacteria perform their magic.....Much like the trickle filter and Fluidised filter, this type of Bio filtration is limited in its ability to provide 'total' breakdown of waste material due to high levels of dissolved O2 again, so it must be supported with other methods to achieve total filtration. The biggest danger 'and one I would be most concerned about' is the massive release of Ammonia and hydrogen sulphide that 'can' occur, in the event of a power cut and the filter being left off for a long duration. After only a few hours some power filters may suffer the total depletion of dissolved O2, and the conversion of nitrate back to ammonia or worse Hydrogen Sulphide which is highly toxic. In such cases, the filter must 'never' be simply re started....It must be removed and thoroughly cleaned out with fresh media added prior to re-connection.

6 Nitrate Filters.

There are various filters of this type on the market, and designs on the web for construction. Some utilising a simple media compartment whereby water is fed through at a very slow rate, whereby O2 is depleted to a level where anaerobic conditions become prevalent. In these cases it is essential to feed the filter on a regular basis utilising a commercially available ‘yeast based’ bacteria food. Adjustment of these filters can take time, and be extremely finicky.....not to mention the dangers of  reverse conversion from Nitrate, back through the stages to Ammonia should the settings or conditions change. Other newer methods employ the use of sulphur beads. In these cases no feeding is necessary. I am of the opinion though that these filters whilst novel, are simply designed as an addition to those methods mentioned above that stop at the Nitrate stage....I.e. Trickle filter-Nitrate filter. If setting up a new system I would always opt for a less fussed and potentially problematic solution where total de-nitrification can be achieved without the need for masses of different equipment. Such as a sand bed/ or combination Refugium/DSB.

7 Live Rock

As this subject is quite in-depth, For Full information on this filtration media Click     here.

Continue to page 2 for details on Chemical Filtration.